My idea was to add height to the tops of the forms tapering towards the shear. But to get added space near the shear where my toes reside and not just at the peak of the deck would mean changing the deck counter somewhat.

Rich-
Your analysis matches mine - for most kayaks where the heels are together at the midline and the toes are pointed to the sides, the extra height is needed 'at the edges'.
That's why I think Etienne's method (an extra strip or two along the sheer to raise the deck) is the way to go.

That's the way some commercial glass boats change from 'Low Volume' to 'High volume' within the same design. One example was some of the Sterling boats where you could order a 'custom fitted' boat. For some more discussion you could check out the 'Model History' section at marinerkayaks.com where Matt Broze discusses how some of their designs evolved.

So raising (or lowering) the sheer is 'in the tradition' in a way!

I also agree with Etienne that you probably don't want to raise the deck aft of your thighs - a low deck aft has a lot of advantages.